Examples with PseudoConstant cbit.vcell.math.PseudoConstant used on opensource projects

Example 1 with PseudoConstant

use of cbit.vcell.math.PseudoConstant in project vcell by virtualcell.

the class FastSystemAnalyzer method refreshSubstitutedRateExps.

/**
 */
private void refreshSubstitutedRateExps() throws MathException, ExpressionException {
    // 
    // refresh PseudoConstants (temp constants involved with fastInvariants)
    // 
    pseudoConstantList.removeAllElements();
    Enumeration<FastInvariant> enum_fi = fastSystem.getFastInvariants();
    while (enum_fi.hasMoreElements()) {
        FastInvariant fi = enum_fi.nextElement();
        Domain domain = new Domain(fastSystem.getSubDomain());
        fi.getFunction().bindExpression(this);
        PseudoConstant pc = new PseudoConstant(getAvailablePseudoConstantName(), fi.getFunction(), domain);
        pseudoConstantList.addElement(pc);
    // System.out.println("FastSystem.refreshSubstitutedRateExps() __C"+i+" = "+fi.getFunction());
    }
    // 
    // build expressions for dependent variables in terms of independent vars
    // and pseudoConstants
    // 
    dependencyExpList.removeAllElements();
    for (int row = 0; row < dependentVarList.size(); row++) {
        Expression exp = new Expression("0.0;");
        // 
        for (int col = 0; col < independentVarList.size(); col++) {
            Variable indepVar = (Variable) independentVarList.elementAt(col);
            RationalExp coefExp = dependencyMatrix.get(row, col).simplify();
            if (!coefExp.isZero()) {
                exp = Expression.add(exp, new Expression(coefExp.infixString() + "*" + indepVar.getName()));
            }
        }
        // 
        for (int col = independentVarList.size(); col < dependencyMatrix.getNumCols(); col++) {
            PseudoConstant pc = (PseudoConstant) pseudoConstantList.elementAt(col - independentVarList.size());
            RationalExp coefExp = dependencyMatrix.get(row, col);
            if (!coefExp.isZero()) {
                exp = Expression.add(exp, new Expression(coefExp.infixString() + "*" + pc.getName()));
            }
        }
        exp.bindExpression(null);
        exp = exp.flatten();
        exp.bindExpression(this);
        // System.out.println("FastSystem.refreshSubstitutedRateExps() "+((Variable)dependentVarList.elementAt(row)).getName()+" = "+exp.toString()+";");
        dependencyExpList.addElement(exp);
    }
    // 
    // flatten functions, then substitute expressions for dependent vars into rate expressions
    // 
    fastRateExpList.removeAllElements();
    // VariableSymbolTable combinedSymbolTable = getCombinedSymbolTable();
    Enumeration<FastRate> enum_fr = fastSystem.getFastRates();
    while (enum_fr.hasMoreElements()) {
        FastRate fr = enum_fr.nextElement();
        Expression exp = new Expression(MathUtilities.substituteFunctions(new Expression(fr.getFunction()), this));
        // System.out.println("FastSystem.refreshSubstitutedRateExps() fast rate before substitution = "+exp.toString());
        for (int j = 0; j < dependentVarList.size(); j++) {
            Variable depVar = (Variable) dependentVarList.elementAt(j);
            Expression subExp = new Expression((Expression) dependencyExpList.elementAt(j));
            exp.substituteInPlace(new Expression(depVar.getName()), subExp);
        }
        exp.bindExpression(null);
        exp = exp.flatten();
        // System.out.println("FastSystem.refreshSubstitutedRateExps() fast rate after substitution  = "+exp.toString());
        exp.bindExpression(this);
        fastRateExpList.addElement(exp);
    }
}

Example 2 with PseudoConstant

use of cbit.vcell.math.PseudoConstant in project vcell by virtualcell.

the class OutputFunctionContext method getEntries.

// public abstract void validateNamingConflicts(String symbolDescription, Class<?> newSymbolClass, String newSymbolName, PropertyChangeEvent e)  throws PropertyVetoException ;
public void getEntries(Map<String, SymbolTableEntry> entryMap) {
    // add all valid entries (variables) from mathdescription
    MathDescription mathDescription = simulationOwner.getMathDescription();
    if (mathDescription != null) {
        Enumeration<Variable> varEnum = mathDescription.getVariables();
        while (varEnum.hasMoreElements()) {
            Variable var = varEnum.nextElement();
            if (!(var instanceof PseudoConstant) && !(var instanceof Constant)) {
                entryMap.put(var.getName(), var);
            }
        }
        for (DataGenerator dataGenerator : mathDescription.getPostProcessingBlock().getDataGeneratorList()) {
            entryMap.put(dataGenerator.getName(), dataGenerator);
        }
    }
    entryMap.put(ReservedVariable.TIME.getName(), ReservedVariable.TIME);
    int dimension = mathDescription.getGeometry().getDimension();
    if (dimension > 0) {
        entryMap.put(ReservedVariable.X.getName(), ReservedVariable.X);
        if (dimension > 1) {
            entryMap.put(ReservedVariable.Y.getName(), ReservedVariable.Y);
            if (dimension > 2) {
                entryMap.put(ReservedVariable.Z.getName(), ReservedVariable.Z);
            }
        }
    }
    // then add list of output functions.
    for (SymbolTableEntry ste : outputFunctionsList) {
        entryMap.put(ste.getName(), ste);
    }
}

Example 3 with PseudoConstant

use of cbit.vcell.math.PseudoConstant in project vcell by virtualcell.

the class FastSystemAnalyzer method refreshSubstitutedRateExps.

/**
 */
private void refreshSubstitutedRateExps() throws MathException, ExpressionException {
    // 
    // refresh PseudoConstants (temp constants involved with fastInvariants)
    // 
    pseudoConstantList.removeAllElements();
    Enumeration<FastInvariant> enum_fi = fastSystem.getFastInvariants();
    while (enum_fi.hasMoreElements()) {
        FastInvariant fi = enum_fi.nextElement();
        fi.getFunction().bindExpression(this);
        PseudoConstant pc = new PseudoConstant(getAvailablePseudoConstantName(), fi.getFunction(), MathMapping_4_8.nullDomain);
        pseudoConstantList.addElement(pc);
    // System.out.println("FastSystem.refreshSubstitutedRateExps() __C"+i+" = "+fi.getFunction());
    }
    // 
    // build expressions for dependent variables in terms of independent vars
    // and pseudoConstants
    // 
    dependencyExpList.removeAllElements();
    for (int row = 0; row < dependentVarList.size(); row++) {
        Expression exp = new Expression("0.0;");
        // 
        for (int col = 0; col < independentVarList.size(); col++) {
            Variable indepVar = (Variable) independentVarList.elementAt(col);
            RationalExp coefExp = dependencyMatrix.get(row, col).simplify();
            if (!coefExp.isZero()) {
                exp = Expression.add(exp, new Expression(coefExp.infixString() + "*" + indepVar.getName()));
            }
        }
        // 
        for (int col = independentVarList.size(); col < dependencyMatrix.getNumCols(); col++) {
            PseudoConstant pc = (PseudoConstant) pseudoConstantList.elementAt(col - independentVarList.size());
            RationalExp coefExp = dependencyMatrix.get(row, col);
            if (!coefExp.isZero()) {
                exp = Expression.add(exp, new Expression(coefExp.infixString() + "*" + pc.getName()));
            }
        }
        exp.bindExpression(null);
        exp = exp.flatten();
        exp.bindExpression(this);
        // System.out.println("FastSystem.refreshSubstitutedRateExps() "+((Variable)dependentVarList.elementAt(row)).getName()+" = "+exp.toString()+";");
        dependencyExpList.addElement(exp);
    }
    // 
    // flatten functions, then substitute expressions for dependent vars into rate expressions
    // 
    fastRateExpList.removeAllElements();
    // VariableSymbolTable combinedSymbolTable = getCombinedSymbolTable();
    Enumeration<FastRate> enum_fr = fastSystem.getFastRates();
    while (enum_fr.hasMoreElements()) {
        FastRate fr = enum_fr.nextElement();
        Expression exp = new Expression(MathUtilities.substituteFunctions(new Expression(fr.getFunction()), this));
        // System.out.println("FastSystem.refreshSubstitutedRateExps() fast rate before substitution = "+exp.toString());
        for (int j = 0; j < dependentVarList.size(); j++) {
            Variable depVar = (Variable) dependentVarList.elementAt(j);
            Expression subExp = new Expression((Expression) dependencyExpList.elementAt(j));
            exp.substituteInPlace(new Expression(depVar.getName()), subExp);
        }
        exp.bindExpression(null);
        exp = exp.flatten();
        // System.out.println("FastSystem.refreshSubstitutedRateExps() fast rate after substitution  = "+exp.toString());
        exp.bindExpression(this);
        fastRateExpList.addElement(exp);
    }
}

Example 4 with PseudoConstant

use of cbit.vcell.math.PseudoConstant in project vcell by virtualcell.

the class FiniteVolumeFileWriter method writeFastSystem.

/*private void writeDataProcessor() throws DataAccessException, IOException, MathException, DivideByZeroException, ExpressionException {
	Simulation simulation = simTask.getSimulation();
	DataProcessingInstructions dpi = simulation.getDataProcessingInstructions();
	if (dpi == null) {
		printWriter.println("DATA_PROCESSOR_BEGIN " + DataProcessingInstructions.ROI_TIME_SERIES);
		printWriter.println("DATA_PROCESSOR_END");
		printWriter.println();
		return;
	}
	
	FieldDataIdentifierSpec fdis = dpi.getSampleImageFieldData(simulation.getVersion().getOwner());	
	if (fdis == null) {
		throw new DataAccessException("Can't find sample image in data processing instructions");
	}
	String secondarySimDataDir = PropertyLoader.getProperty(PropertyLoader.secondarySimDataDirProperty, null);	
	DataSetControllerImpl dsci = new DataSetControllerImpl(new NullSessionLog(),null,userDirectory.getParentFile(),secondarySimDataDir == null ? null : new File(secondarySimDataDir));
	CartesianMesh origMesh = dsci.getMesh(fdis.getExternalDataIdentifier());
	SimDataBlock simDataBlock = dsci.getSimDataBlock(null,fdis.getExternalDataIdentifier(), fdis.getFieldFuncArgs().getVariableName(), fdis.getFieldFuncArgs().getTime().evaluateConstant());
	VariableType varType = fdis.getFieldFuncArgs().getVariableType();
	VariableType dataVarType = simDataBlock.getVariableType();
	if (!varType.equals(VariableType.UNKNOWN) && !varType.equals(dataVarType)) {
		throw new IllegalArgumentException("field function variable type (" + varType.getTypeName() + ") doesn't match real variable type (" + dataVarType.getTypeName() + ")");
	}
	double[] origData = simDataBlock.getData();	

	String filename = SimulationJob.createSimulationJobID(Simulation.createSimulationID(simulation.getKey()), simulationJob.getJobIndex()) + FieldDataIdentifierSpec.getDefaultFieldDataFileNameForSimulation(fdis.getFieldFuncArgs());
	
	File fdatFile = new File(userDirectory, filename);
	
	
	DataSet.writeNew(fdatFile,
			new String[] {fdis.getFieldFuncArgs().getVariableName()},
			new VariableType[]{simDataBlock.getVariableType()},
			new ISize(origMesh.getSizeX(),origMesh.getSizeY(),origMesh.getSizeZ()),
			new double[][]{origData});
	printWriter.println("DATA_PROCESSOR_BEGIN " + dpi.getScriptName());
	printWriter.println(dpi.getScriptInput());
	printWriter.println("SampleImageFile " + fdis.getFieldFuncArgs().getVariableName() + " " + fdis.getFieldFuncArgs().getTime().infix() + " " + fdatFile);
	printWriter.println("DATA_PROCESSOR_END");
	printWriter.println();

	
}
*/
/**
 *# fast system dimension num_dependents
 *FAST_SYSTEM_BEGIN 2 2
 *INDEPENDENT_VARIALBES rf r
 *DEPENDENT_VARIALBES rB rfB
 *
 *PSEUDO_CONSTANT_BEGIN
 *__C0 (rfB + rf);
 *__C1 (r + rB);
 *PSEUDO_CONSTANT_END
 *
 *FAST_RATE_BEGIN
 * - ((0.02 * ( - ( - r + __C1) - ( - rf + __C0) + (20.0 * ((x > -3.0) && (x < 3.0) && (y > -5.0) && (y < 5.0))) + _VCell_FieldData_0) * rf) - (0.1 * ( - rf + __C0)));
 *((0.02 * r * ( - ( - r + __C1) - ( - rf + __C0) + (20.0 * ((x > -3.0) && (x < 3.0) && (y > -5.0) && (y < 5.0))) + _VCell_FieldData_0)) - (0.1 * ( - r + __C1)));
 *FAST_RATE_END
 *
 *FAST_DEPENDENCY_BEGIN
 *rB ( - r + __C1);
 *rfB ( - rf + __C0);
 *FAST_DEPENDENCY_END
 *
 *JACOBIAN_BEGIN
 * - (0.1 + (0.02 * (1.0 + (0.0 * ((x > -3.0) && (x < 3.0) && (y > -5.0) && (y < 5.0)))) * rf) + (0.02 * ( - ( - r + __C1) - ( - rf + __C0) + (20.0 * ((x > -3.0) && (x < 3.0) && (y > -5.0) && (y < 5.0))) + _VCell_FieldData_0)));
 * - (0.02 * (1.0 + (0.0 * ((x > -3.0) && (x < 3.0) && (y > -5.0) && (y < 5.0)))) * rf);
 *(0.02 * r * (1.0 + (0.0 * ((x > -3.0) && (x < 3.0) && (y > -5.0) && (y < 5.0)))));
 *(0.1 + (0.02 * ( - ( - r + __C1) - ( - rf + __C0) + (20.0 * ((x > -3.0) && (x < 3.0) && (y > -5.0) && (y < 5.0))) + _VCell_FieldData_0)) + (0.02 * r * (1.0 + (0.0 * ((x > -3.0) && (x < 3.0) && (y > -5.0) && (y < 5.0))))));
 *JACOBIAN_END
 *
 *FAST_SYSTEM_END
 * @throws ExpressionException
 * @throws MathException
 */
private void writeFastSystem(SubDomain subDomain) throws MathException, ExpressionException {
    VariableDomain variableDomain = (subDomain instanceof CompartmentSubDomain) ? VariableDomain.VARIABLEDOMAIN_VOLUME : VariableDomain.VARIABLEDOMAIN_MEMBRANE;
    FastSystem fastSystem = subDomain.getFastSystem();
    if (fastSystem == null) {
        return;
    }
    FastSystemAnalyzer fs_analyzer = new FastSystemAnalyzer(fastSystem, simTask.getSimulationJob().getSimulationSymbolTable());
    int numIndep = fs_analyzer.getNumIndependentVariables();
    int numDep = fs_analyzer.getNumDependentVariables();
    int numPseudo = fs_analyzer.getNumPseudoConstants();
    printWriter.println("# fast system dimension num_dependents");
    printWriter.println("FAST_SYSTEM_BEGIN " + numIndep + " " + numDep);
    if (numIndep != 0) {
        printWriter.print("INDEPENDENT_VARIALBES ");
        Enumeration<Variable> enum1 = fs_analyzer.getIndependentVariables();
        while (enum1.hasMoreElements()) {
            Variable var = enum1.nextElement();
            printWriter.print(var.getName() + " ");
        }
        printWriter.println();
    }
    if (numDep != 0) {
        printWriter.print("DEPENDENT_VARIALBES ");
        Enumeration<Variable> enum1 = fs_analyzer.getDependentVariables();
        while (enum1.hasMoreElements()) {
            Variable var = enum1.nextElement();
            printWriter.print(var.getName() + " ");
        }
        printWriter.println();
    }
    printWriter.println();
    if (numPseudo != 0) {
        printWriter.println("PSEUDO_CONSTANT_BEGIN");
        Enumeration<PseudoConstant> enum1 = fs_analyzer.getPseudoConstants();
        while (enum1.hasMoreElements()) {
            PseudoConstant pc = enum1.nextElement();
            printWriter.println(pc.getName() + " " + subsituteExpression(pc.getPseudoExpression(), fs_analyzer, variableDomain).infix() + ";");
        }
        printWriter.println("PSEUDO_CONSTANT_END");
        printWriter.println();
    }
    if (numIndep != 0) {
        printWriter.println("FAST_RATE_BEGIN");
        Enumeration<Expression> enum1 = fs_analyzer.getFastRateExpressions();
        while (enum1.hasMoreElements()) {
            Expression exp = enum1.nextElement();
            printWriter.println(subsituteExpression(exp, fs_analyzer, variableDomain).infix() + ";");
        }
        printWriter.println("FAST_RATE_END");
        printWriter.println();
    }
    if (numDep != 0) {
        printWriter.println("FAST_DEPENDENCY_BEGIN");
        Enumeration<Expression> enum_exp = fs_analyzer.getDependencyExps();
        Enumeration<Variable> enum_var = fs_analyzer.getDependentVariables();
        while (enum_exp.hasMoreElements()) {
            Expression exp = enum_exp.nextElement();
            Variable depVar = enum_var.nextElement();
            printWriter.println(depVar.getName() + " " + subsituteExpression(exp, fs_analyzer, variableDomain).infix() + ";");
        }
        printWriter.println("FAST_DEPENDENCY_END");
        printWriter.println();
    }
    if (numIndep != 0) {
        printWriter.println("JACOBIAN_BEGIN");
        Enumeration<Expression> enum_fre = fs_analyzer.getFastRateExpressions();
        while (enum_fre.hasMoreElements()) {
            Expression fre = enum_fre.nextElement();
            Enumeration<Variable> enum_var = fs_analyzer.getIndependentVariables();
            while (enum_var.hasMoreElements()) {
                Variable var = enum_var.nextElement();
                Expression exp = subsituteExpression(fre, fs_analyzer, variableDomain).flatten();
                Expression differential = exp.differentiate(var.getName());
                printWriter.println(subsituteExpression(differential, fs_analyzer, variableDomain).infix() + ";");
            }
        }
        printWriter.println("JACOBIAN_END");
        printWriter.println();
    }
    printWriter.println("FAST_SYSTEM_END");
    printWriter.println();
}

Example 5 with PseudoConstant

use of cbit.vcell.math.PseudoConstant in project vcell by virtualcell.

the class OutputFunctionContext method getEntry.

public SymbolTableEntry getEntry(java.lang.String identifierString) {
    // 
    // use MathDescription as the primary SymbolTable, just replace the Constants with the overrides.
    // 
    SymbolTableEntry ste = null;
    MathDescription mathDescription = simulationOwner.getMathDescription();
    if (mathDescription != null) {
        ste = mathDescription.getEntry(identifierString);
        if (ste != null && !(ste instanceof PseudoConstant) && !(ste instanceof Constant)) {
            return ste;
        }
        ste = mathDescription.getPostProcessingBlock().getDataGenerator(identifierString);
        if (ste instanceof DataGenerator) {
            return ste;
        }
    }
    // see if it is an output function.
    ste = getOutputFunction(identifierString);
    return ste;
}